Biology subjects

Dubey, M.

Publications and source records attributed to Dubey, M..

17 recordsLinked to original sources

bioRxiv2026

Divisive normalization in mouse V1 is unchanged by increased thalamocortical short-term depression

Divisive normalization describes how neuronal responses are scaled by the activity of a broader pool of inputs and accounts for several nonlinear response properties in primary visual cortex (V1). It accurately describes contrast gain control, as well as the response to overlapping gratings. Nevertheless, how this computation is performed by the brain is unclear. One mechanism suggested to underlie divisive normalization in V1 is short-term depression (STD) at thalamocortical synapses. Here, we used a Vglut2-Cre dependent heterozygous deletion of Stxbp1 in mice as an in vivo model for increased STD. This enabled us to test whether STD is responsible for divisive normalization in V1. As expected, responses were shorter in the mutant mice compared to wild-type siblings. Although we did find other differences in visual responses, notably in direction selectivity and response linearity, neither the contrast response function, nor the amount of cross orientation suppression differed between the two groups. We conclude that STD is likely not involved in divisive normalization of visual responses in mouse V1. Instead, short-term plasticity shapes the temporal integration through which selective cortical responses are constructed.

neuroscience↗

bioRxiv2026

Homothallic or heterothallic? A genomic investigation into the sexual capabilities of the ascomycete fungus Clonostachys rosea

Modes of reproduction and sexual strategies strongly influence the genetic diversity and evolutionary potential of a species. The ascomycete fungus Clonostachys rosea is reported to be homothallic (sexually self-fertile), although a rapid decay of genome-wide linkage disequilibrium is also reported, something that is not in line with an obligate homothallic mode of reproduction. To investigate this phenomenon, we identified the mating-type (MAT1) locus in 66 genome-sequenced C. rosea strains under the hypothesis that each strain contains genes from both MAT1 idiomorphs. Eleven strains indeed contained both MAT1-1 and MAT1-2 genes, suggesting homothallism. However, most strains harboured either MAT1-1 or MAT1-2 genes and co-existed in North America, Europe and China, suggesting heterothallism. The MAT1 locus of heterothallic strains was highly conserved, and the linkage disequilibrium half decay distance was 1050 bp, suggesting sexual outcrossing. The presence of conserved MAT1-1 or MAT1-2 idiomorphs in strains of other Clonostachys species shows that heterothallism is likely the ancestral state. A phylogenetic analysis of 2800 single-copy orthologous genes revealed that homothallic and heterothallic strains separated in two well-supported clades, indicating a single lineage of homothallic C. rosea, likely originating in South America, followed by intercontinental dispersal. Homothallic C. rosea strains displayed higher nucleotide diversity than heterothallic strains, indicating a lack of outcrossing. This unique case of both homothallic and heterothallic lineages within the same species provides an opportunity to study the genomic consequences of selfing in very closely related strains.

evolutionary biology↗

bioRxiv2024

Plant genotype-specific modulation of Clonostachys rosea-mediated biocontrol of septoria tritici blotch disease on wheat

BackgroundBeneficial microorganisms can act as biological control agents (BCAs) by directly targeting pathogens or indirectly by enhancing the plants defense mechanisms against pathogens. However, efficiencies with which plants benefit from BCAs vary, potentially because of genetic variation in plants for plant-BCA compatibility. The aim of this study was to explore the genetic variation in winter wheat for modulation of Clonostachys rosea-mediated biocontrol of septoria tritici blotch disease caused by the fungal pathogen Zymoseptoria tritici. ResultsIn total, 202 winter wheat genotypes, including landraces and old cultivars grown from 1900 onwards in the Scandinavian countries, were tested under greenhouse-controlled conditions. Foliar spray applications of the pathogen and the fungal BCA in two treatments, i.e., Z. tritici (Zt) alone and Z. tritici along with C. rosea (ZtCr) were used to assess the disease progress over time. The absence and presence of C. rosea in Zt and ZtCr, respectively, allowed the dissection of variation for plant disease resistance and biocontrol efficacy. The study showed significant phenotypic variation among plant genotypes for disease progression in both Zt and ZtCr treatments. Moreover, disease progress for individual plant genotypes differed significantly between the two treatments, indicating a plant genotype-dependent variation in biocontrol efficacy. For the phenotypic variation in disease progress and biocontrol efficacy, a genome-wide association study using a 20K single-nucleotide polymorphism (SNP) marker array was also performed. In total, five distinct SNP markers associated with disease resistance and four SNP markers associated with C. rosea biocontrol efficacy were identified. ConclusionsThis work serves as a foundation to further characterize the genetic basis of plant-BCA interactions, facilitating opportunities for concurrent breeding for disease resistance and biocontrol efficacy.

plant biology↗

bioRxiv2024

Inferring Bacterial Interspecific Interactions from Microcolony Growth Expansion

Interactions between species are thought to be crucial for modulating their growth and behaviour within communities, and determinant for the emergence of community functions. Several different interaction concepts exist, but there is no consensus on how interactions should be quantified and integrated in community growth theory. Here we expand on existing concepts of real-time measurements of pure culture microcolony growth to develop and benchmark coculture microcolony experiments, and show how these can both parametrize growth kinetic and interspecific interaction effects. We follow surface growth by time-lapse microscopy of fluorescently tagged Pseudomonas putida and Pseudomonas veronii under substrate competition with succinate, or under substrate indifference with D-mannitol and putrescine. Monoculture-grown microcolonies showed substrate concentration dependent expansion rates as expected from Monod relations, whereas individual microcolony yields were strongly dependent on densities and spatial positioning of founder cells. Maximum specific growth rates in cocultures under substrate competition were diminished by ca. 15%, which was seeding-density independent. The collective P. putida population dominated growth over that of P. veronii, but with 27% yield loss under competition compared to monoculture growth; and 90% for that of P. veronii. Incidental local reversal of competition was observed where P. veronii microcolonies profited at the detriment of P. putida, and between 9 and 43% of P. veronii microcolonies grew bigger than expected from bulk competition, depending on seeding density. Simulations with a cell-agent Monod surface growth model suggested that colony expansion rate decrease in competitive coculture is caused by metabolite cross-feeding, which was supported by exometabolite analysis during and after growth of the strains on their individual or swapped supernatant. Coculture microcolony growth experiments thus provide a flexible platform for analysis of kinetic and interspecific interactions, expanding from individual microcolony phenotypic effects to averaged behaviour across all microcolony pairs. The system in theory is scalable to follow real-time growth of multiple species simultaneously into communities.

microbiology↗

bioRxiv2024

SREBP-mediated gene expression regulation is essential for the intrinsic fungicide tolerance and antagonism in the fungal biocontrol agent Clonostachys rosea

Sterol regulatory element-binding proteins (SREBPs) are a family of transcription factors known to regulate sterol biosynthesis and homeostasis in fungi. For this reason they have a role in several biological processes, including virulence, fungicide tolerance, hypoxia adaptation, lipid and carbohydrate metabolisms, and iron homeostasis. While the biological function of SREBPs in yeast and filamentous fungal species pathogenic to humans and plants is known, their role in fungal biocontrol agents (BCAs) is still elusive. This study aimed to investigate the biological and regulatory function of SREBPs in the BCA Clonostachys rosea, with a focus on their role in fungicide tolerance, hypoxia adaptation and antagonisms. The C. rosea genome contains two genes (sre1 and sre2) coding for SREBPs and one gene each coding for Insulin induced gene (INSIG) and SREBP cleavage-activating protein (SCAP), required for SREBP-mediated ergosterol biosynthesis in fungi. Deletion of sre1 resulted in mutants with pleiotropic effects, including the reduced ability to grow on media supplemented with proline (active ingredient prothioconazole) and cantus (active ingredient boscalid) fungicides, hypoxia mimicking agent CoCl2, cell wall stressor SDS, and increased growth rate on medium supplemented with caffeine, compared with C. rosea wild type (WT). In addition, the antagonistic ability against the fungal hosts Botrytis cinerea and Rhizoctonia solani was affected when sre1 was deleted. However, no significant difference between sre2 deletion strains and C. rosea WT was found for any of the tested phenotypes. To investigate the regulatory role of SRE1, the transcriptome of C. rosea WT and a sre1 deletion strain was analyzed. The transcriptome analysis identified differentially expressed genes in the sre1 deletion strain associated with carbohydrate and lipid metabolism, respiration, iron homeostasis, and xenobiotic tolerance. Moreover, genes coding for polyketide synthases and chitinases with a proven antimicrobial role were downregulated in the mutant, corroborating the reduced antagonism phenotypes. In summary, this work sheds light on the regulation role of transcription factor SRE1 while also exploring its effect on regulating the antagonistic activity and fungicide resistance of C. rosea, giving us helpful knowledge to design applications of this organism in IPM strategies.

microbiology↗

bioRxiv2023

Niche Availability and Competitive Facilitation Control Proliferation of Bacterial Strains Intended for Soil Microbiome Interventions

Microbiome engineering, the rational manipulation of microbial communities and their habitats, is considered a crucial strategy to revert dysbiosis. However, the concept is in its infancy and lacks experimental support. Here we study the ecological factors controlling the proliferation of focal bacterial inoculants into taxa-complex soil communities and their impact on resident microbiota. We demonstrate using standardized soil microbiomes with different growth phases that the proliferation of typical soil inoculants depends on niche competition. By adding an artificial, inoculant selective niche to soil we improve inoculant proliferation and show by metatranscriptomics to give rise to a conjoint metabolic network in the soil microbiome. Furthermore, using random paired growth assays we demonstrate that, in addition to direct competition, inoculants lose competitiveness with soil bacteria because of metabolite sharing. Thus, the fate of inoculants in soil is controlled by niche availability and competitive facilitation, which may be manipulated by selective niche generation. TeaserTypical bacterial inoculants for soil microbiome engineering suffer from facilitating growth of native resident microorganisms

ecology↗

bioRxiv2023

Dicer-mediated RNA silencing is the key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions

The intricate molecular interplay between beneficial fungi and plants is vital to plant growth promotion and induced defense response. This study explored the role of DCL-mediated RNA silencing in the interaction between the biocontrol fungus Clonostachys rosea and wheat roots. We investigated the impact of DCL (Dicer-like) gene deletions in C. rosea on its root colonization ability. Our results revealed that the deletion of dcl2 significantly enhanced C. rosea biomass on wheat roots, indicating a pivotal role of DCL2 in root colonization. Transcriptome sequencing of C. rosea and wheat during their interactions unveiled extensive gene expression changes. In wheat, genes related to stress responses were upregulated during C. rosea interactions, while genes associated with plant cell wall modification and metabolic processes were downregulated, suggesting complex regulatory responses and a trade-off between defense mechanisms and growth promotion. Deletion of C. rosea dcl1 and dcl2 altered the transcriptomic responses of wheat roots during interactions. Wheat genes associated with stress responses were downregulated during interactions with DCL deletion strains. In contrast, genes involved in metabolic processes and growth were upregulated, emphasizing the cross-kingdom regulatory role of C. rosea small RNAs (sRNAs). We identified 18 wheat miRNAs responsive to C. rosea interactions. Furthermore, we identified 24 endogenous and six cross-kingdom potential gene targets for seven and five differentially expressed miRNAs, supported by their inverse gene expression pattern. In C. rosea, we found a large transcriptional reprogramming of genes during interaction with wheat roots. The upregulated genes were associated with carbohydrate and polysaccharide catabolic processes, membrane transporters and effectors. Conversely, downregulated genes were mainly associated with transition metal ion transport and homeostasis processes. The deletion of dcl1 and dcl2 had significant effects on gene expression. A higher number of genes upregulated in WT during the interaction were restored in DCL deletion mutants, suggesting DCL-mediated gene expression regulation. Furthermore, we identified 21 differentially expressed micro-RNA-like RNAs (milRNAs) in C. rosea; nine were DCL-dependent. They had putative gene targets in C. rosea, including transcription factors, effectors, transporters, and enzymes involved in specialized metabolite production. Cross-kingdom RNA silencing was also observed, with seven DCL-dependent C. rosea milRNAs potentially targeting 29 genes in wheat. These findings provide valuable insights into the molecular mechanisms underlying the beneficial interaction between fungi and plant roots. In addition, the study shed light on the role of sRNA-mediated gene regulation in the C. rosea-wheat interaction, with potential implications for sustainable agriculture and biocontrol strategies.

genomics↗

bioRxiv2023

Psycho-spatially distinct stressors prompt distinct behavioral strategies through a cell type-specific brain circuit

Adaptive behavioral responses to stressors are critical for survival. However, which brain areas orchestrate switching the appropriate stress responses to distinct contexts is an open question. This study aimed to identify the cell type-specific brain circuitry governing the selection of distinct behavioral strategies in response to stressors. Through novel mouse behavior paradigms, we observed distinct stressor-evoked behaviors in two psycho-spatially distinct contexts, characterized by stressors inside or outside the safe zone. The identification of brain regions activated in both conditions revealed the involvement of the dorsomedial hypothalamus (DMH). Further investigation using optogenetics, chemogenetics, and photometry uncovered that glutamatergic projections from the DMH to periaqueductal gray (PAG) mediated responses to inside-stressors, while GABAergic projections, particularly from tachykinin1-expressing neurons, played a crucial role in coping with outside-stressors. These findings elucidate the role of cell type-specific circuitry from the DMH to the PAG in shaping behavioral strategies in response to stressors. These findings have the potential to advance our understanding of fundamental neurobiological processes and inform the development of novel approaches for managing context-dependent and anxiety-associated pathological conditions such as agoraphobia and claustrophobia.

neuroscience↗

bioRxiv2023

Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding

When bacterial species with the same resource preferences share the same growth environment, it is commonly believed that direct competition will arise. A large variety of competition and more general interaction models have been formulated, but what is currently lacking are models that link mono-culture growth kinetics and community growth under inclusion of emerging biological interactions, such as metabolite cross-feeding. In order to understand and mathematically describe the nature of potential cross-feeding interactions, we design experiments where two bacterial species Pseudomonas putida and Pseudomonas veronii grow in liquid medium either in mono- or as co-culture in a resource-limited environment. We measure population growth under single substrate competition or with double species-specific substrates (substrate indifference), and starting from varying cell ratios of either species. Using experimental data as input, we first consider a mean-field model of resource-based competition, which captures well the empirically observed growth rates for mono-cultures, but fails to correctly predict growth rates in co-culture mixtures, in particular for skewed starting species ratios. Based on this, we extend the model by cross-feeding interactions where the consumption of substrate by one consumer produces metabolites that in turn are resources for the other consumer, thus leading to positive feedback loops in the species system. Two different cross-feeding options were considered, which either lead to constant metabolite cross-feeding, or to a regulated form, where metabolite utilization is activated with rates according to either a threshold or a Hill function, dependent on metabolite concentration. Both mathematical proof and experimental data indicate regulated cross-feeding to be the preferred model over constant metabolite utilization, with best co-culture growth predictions in case of high Hill coefficients, close to binary (on/off) activation states. This suggests that species use the appearing metabolite concentrations only when they are becoming high enough; possibly as a consequence of their lower energetic content than the primary substrate. Metabolite sharing was particularly relevant at unbalanced starting cell ratios, causing the minority partner to proliferate more than expected from the competitive substrate because of metabolite release from the majority partner. This effect thus likely quells immediate substrate competition and may be important in natural communities with typical very skewed relative taxa abundances and slower-growing taxa. In conclusion, the regulated bacterial interaction network correctly describes species substrate growth reactions in mixtures with few kinetic parameters that can be obtained from mono-culture growth experiments. 1 Author summaryCorrectly predicting growth of communities of diverse bacterial taxa remains a challenge, because of the very different growth properties of individual members and their myriads of interactions that can influence growth. Here we tried to improve and empirically validate mathematical models that combine theory of bacterial growth kinetics (i.e., Monod models) with mathematical definition of interaction parameters. We focused in particular on common cases of shared primary substrates (i.e., competition) and independent substrates (i.e., indifference) in an experimental system consisting of one fast-growing and one slower growing Pseudomonas species. Growth kinetic parameters derived from mono-culture experiments included in a Monod-type consumer-resource model explained some 75% of biomass formation of either species in co-culture, but underestimated the observed growth improvement when either of the species started as a minority compared to the other. This suggested an in important role of cross-feeding, whereby released metabolites from one of the partners is utilized by the other. Inclusion of cross-feeding feedback in the two-species Monod growth model largely explained empirical data at all species-starting ratios, in particular when cross-feeding is activated in almost binary manner as a function of metabolite concentration. Our results also indicate the importance of cross-feeding for minority taxa, which can explain their survival despite being poorly competitive.

microbiology↗

bioRxiv2022

Comparative small RNA and degradome sequencing provide new insights into antagonistic interactions in the biocontrol fungus Clonostachys rosea

Necrotrophic mycoparasitism is an intricate process involving recognition, physical mycelial contact and killing of host fungi (mycohosts). During such interactions, mycoparasites undergo a complex developmental process involving massive regulatory changes of gene expression to produce a range of chemical compounds and proteins that contribute to the parasitism of the mycohosts. Small-RNAs (sRNAs) are vital components of post-transcriptional gene regulation, although their role in gene expression regulation during mycoparasitism remain understudied. Here, we investigated the role of sRNA-mediated gene regulation in mycoparasitism by performing sRNA and degradome tags sequencing of the mycoparasitic fungus Clonostachys rosea interacting with the plant pathogenic mycohosts Botrytis cinerea and Fusarium graminearum at two time points. The majority of differentially expressed sRNAs were down-regulated during the interactions with the mycohosts compared to a C. rosea self-interaction control, thus allowing de-suppression (up-regulation) of mycohost-responsive genes. Degradome analysis showed a positive correlation between high degradome counts and antisense sRNA mapping and led to the identification of 201 sRNA-mediated gene targets for 282 differentially expressed sRNAs. Analysis of sRNA gene targets revealed that the regulation of genes coding for membrane proteins was a common response against both mycohosts. While the regulation of genes involved in oxidative stress tolerance and cellular metabolic and biosynthetic processes was exclusive against F. graminearum highlighting common and mycohosts-specific gene regulation of C. rosea. By combining these results with transcriptome data collected in similar experimental conditions during a previous study, we expand the understanding of the role of sRNA in regulating interspecific fungal interactions and mycoparasitism. ImportanceSmall-RNAs (sRNAs) are emerging as key players in pathogenic and symbiotic fungus-plant interactions, however, their role in fungal-fungal interactions remains elusive. In this study, we employed the necrotrophic mycoparasite Clonostachys rosea and plant pathogenic mycohots Botrytis cinerea and Fusarium graminearum and investigated the sRNA-mediated gene regulation in mycoparasitic interactions. The combined approach of sRNA and degradome tag sequencing identified 201 sRNA-mediated putative gene targets for 282 differentially expressed sRNAs highlighting the role of sRNA-mediated regulation of mycoparasitism in C. rosea. We also identified 36 known and 13 novel miRNAs and their potential gene targets at endogenous level, and at a cross-species level in B. cinerea and F. graminearum indicating a role of cross-species RNAi in mycoparasitism, representing a novel mechanism in biocontrol interactions. Furthermore, we showed that C. rosea adapts its transcriptional response, and thereby its interaction mechanisms, based on the interaction stages and identity of the mycohost.

microbiology↗

bioRxiv2021

The role of antigen recognition in the γδ T cell response at the controlled stage of M. tuberculosis infection.

{gamma}{delta} T cells contribute to host immune defense uniquely; but how they function in different stages (e.g., acute versus chronic) of a specific infection remains unclear. As the role of{gamma}{delta} T cells in early, active Mycobacterium tuberculosis (Mtb) infection is well documented, we focused on elucidating the{gamma}{delta} T cell response in persistent or controlled Mtb infection. Systems analysis of circulating{gamma}{delta} T cells from a South African adolescent cohort identified a distinct population of CD8+{gamma}{delta} T cells that expanded in this state. These cells had features indicative of persistent antigenic exposure but were robust cytolytic effectors and cytokine/chemokine producers. While these{gamma}{delta} T cells displayed an attenuated response to TCR-mediated stimulation, they expressed Natural Killer (NK) cell receptors and had robust CD16 (Fc{gamma}RIIIA)-mediated cytotoxic response, suggesting alternative ways for{gamma}{delta} T cells to control this stage of the infection. Despite this NK- like functionality, the CD8+{gamma}{delta} T cells consisted of highly expanded clones, which utilized TCRs with different V{gamma}/{delta} pairs. Theses TCRs could respond to an Mtb-lysate, but not to phosphoantigens, which are components of Mtb-lysate that activate{gamma}{delta} T cells in acute Mtb infection, indicating that the CD8+{gamma}{delta} T cells were induced in a stage-specific, antigen-driven manner. Indeed, trajectory analysis showed that these{gamma}{delta} T cells arose from naive cells that had traversed distinct differentiation paths in this infection stage. Importantly, increased levels of CD8+{gamma}{delta} T cells were also found in other chronic inflammatory conditions, including cardiovascular disease and cancer, suggesting that persistent antigenic exposure may lead to similar{gamma}{delta} T cell responses.

immunology↗

bioRxiv2021

Myelin speeds cortical oscillations by consolidating phasic parvalbumin-mediated inhibition

Parvalbumin-positive (PV+) {gamma}-aminobutyric acid (GABA) interneurons are critically involved in producing rapid network oscillations and cortical microcircuit computations but the significance of PV+ axon myelination to the temporal features of inhibition remains elusive. Here using toxic and genetic models of demyelination and dysmyelination, respectively, we find that loss of compact myelin reduces PV+ interneuron presynaptic terminals, increases failures and the weak phasic inhibition of pyramidal neurons abolishes optogenetically driven gamma oscillations in vivo. Strikingly, during periods of quiet wakefulness selectively theta rhythms are amplified and accompanied by highly synchronized interictal epileptic discharges. In support of a causal role of impaired PV-mediated inhibition, optogenetic activation of myelin-deficient PV+ interneurons attenuated the power of slow theta rhythms and limited interictal spike occurrence. Thus, myelination of PV axons is required to consolidate fast inhibition of pyramidal neurons and enable behavioral state-dependent modulation of local circuit synchronization.

neuroscience↗

bioRxiv2021

The role of Dicer-dependent RNA interference in regulating cross-species communication during fungus-fungus interactions

Dicer-like (DCL) proteins play a vital role in transcriptional and post-transcriptional gene silencing, also known as RNA interference (RNAi), by cleaving double-stranded RNAs or single-stranded RNAs with stem-loop structures into small RNAs. Although DCL-mediated RNAi can regulate interspecific communication between pathogenic/mutualistic organisms and their hosts, its role in parasitic fungus-fungus interactions is yet to be investigated. In this study, we deleted dcl genes in the mycoparasitic fungus Clonostachys rosea and analyzed the transcriptome and secondary metabolome to characterize the regulatory functions of DCL-dependent RNAi in mycoparasitism. Deletion of dcl2 resulted in a mutant with reduced growth rate, pigment production and antagonism towards the plant pathogenic fungus Botrytis cinerea. Moreover, the {Delta}dcl2 mutant displayed a reduced ability to control fusarium foot rot disease on wheat, caused by Fusarium graminearum, and reduced production of 62 secondary metabolites (SM) including yellow-coloured sorbicillinoids. Transcriptome sequencing of the in vitro interaction between the C. rosea {Delta}dcl2 strain and B. cinerea or F. graminearum identified downregulation of genes coding for transcription factors, membrane transporters, hydrolytic enzymes and SM biosynthesis enzymes putatively involved in antagonistic interactions, in comparison with the C. rosea wild type interaction. Sixty-one putative novel microRNA-like RNAs (milRNAs) were identified in C. rosea, and 11 was upregulated in the {Delta}dcl2 mutant. In addition to putative endogenous gene targets, these DCL2-dependent milRNAs were predicted to target B. cinerea and F. graminearum virulence factor genes, which showed an increased expression during interaction with the {Delta}dcl2 mutant incapable of producing the targeting milRNAs. This paper constitutes the first step in elucidating the role of RNAi in mycoparasitism, with important implications for biological control of plant diseases. This study further indicates a possible cross-species regulatory activity of fungal milRNAs, emphasizing a novel role of RNAi in fungal interactions and ecology. Author summaryRNA interference (RNAi) is a conserved cellular mechanism mediated by small RNAs (sRNAs) regulating biological processes through the targeted destruction or modulation of RNA filaments necessary for protein synthesis. Dicer-like endoribonucleases (DCL) play a vital role in the RNAi pathway by generating sRNAs. In this study, we identified two DCL-encoding genes in the mycoparasitic fungus Clonostachys rosea and investigated a role of DCL-mediated RNAi in interference interactions between Clonostachys rosea and the two important fungal pathogens Botrytis cinerea and Fusarium graminearum (here called mycohost). Using transcriptome (sRNA and mRNA) sequencing and secondary metabolome analysis approach, we found that the dcl mutants were not able to produce 11 sRNAs predicted to finetune the regulatory network of genes known to be involved in production of hydrolytic enzymes, antifungal compounds, and membrane transporters needed for antagonistic action of C. rosea. We also found C. rosea sRNAs putatively targeting known virulence factors in the mycohost, indicating RNAi-mediated cross-species communication. Our study expanded the understanding of underlying mechanisms of cross-species communication during interference interactions and showed that DCL-mediated RNAi is an important regulator of parasitic fungus-fungus interactions. The results pose the base for future works studying the role of DCL-based cross-species RNAi in fungal interactions.

genomics↗

bioRxiv2021

Divergent early antibody responses define COVID-19 disease trajectories

A damaging inflammatory response is strongly implicated in the pathogenesis of severe COVID-19 but mechanisms contributing to this response are unclear. In two prospective cohorts, early non-neutralizing, afucosylated, anti-SARS-CoV-2 IgG predicted progression from mild, to more severe COVID-19. In contrast to the antibody structures that predicted disease progression, antibodies that were elicited by mRNA SARS-CoV-2 vaccines were low in Fc afucosylation and enriched in sialylation, both modifications that reduce the inflammatory potential of IgG. To study the biology afucosylated IgG immune complexes, we developed an in vivo model which revealed that human IgG-Fc{gamma}R interactions can regulate inflammation in the lung. Afucosylated IgG immune complexes induced inflammatory cytokine production and robust infiltration of the lung by immune cells. By contrast, vaccine elicited IgG did not promote an inflammatory lung response. Here, we show that IgG-Fc{gamma}R interactions can regulate inflammation in the lung and define distinct lung activities associated with the IgG that predict severe COVID-19 and protection against SARS-CoV-2. One Sentence SummaryDivergent early antibody responses predict COVID-19 disease trajectory and mRNA vaccine response and are functionally distinct in vivo.

immunology↗

bioRxiv2021

Spray-induced gene silencing as a potential tool to control potato late blight disease

Phytophthora infestans causes late blight disease on potato and tomato and is currently controlled by resistant cultivars or intensive fungicide spraying. Here, we investigated an alternative means for late blight control by spraying potato leaves with double-stranded RNAs (dsRNA) that target P. infestans genes that are essential for infection. Through confocal microscopy, we show that the sporangia of P. infestans expressing Green Fluorescent Protein (GFP) can take up in vitro synthesized dsRNAs homologous to GFP directly from their surroundings, including leaves, which leads to the reduced relative expression of GFP. We further demonstrate the potential of spray induced gene silencing (SIGS) in controlling potato late blight disease by targeting developmentally important genes in P.infestans such as guanine-nucleotide binding (G) protein {beta}-subunit (PiGPB1), haustorial membrane protein (PiHmp1), cutinase (PiCut3), and endo-1,3(4)-{beta}-glucanase (PiEndo3). Our results demonstrate that SIGS can be potentially used to mitigate potato late blight; however, the degree of disease control is dependent on the selection of the target genes.

plant biology↗

bioRxiv2021

Complement-associated loss of CA2 inhibitory synapses in the demyelinated hippocampus impairs memory

The complement system is implicated in synapse loss in the MS hippocampus, but the functional consequences of synapse loss remain poorly understood. Here, in post-mortem MS hippocampi with demyelination we find that deposits of the complement component C1q are enriched in the CA2 subfield, are linked to loss of inhibitory synapses and are significantly higher in MS patients with cognitive impairments compared to those with preserved cognitive functions. Using the cuprizone mouse model of demyelination, we corroborated that C1q deposits are highest within the demyelinated dorsal hippocampal CA2 pyramidal layer, and co-localized with inhibitory synapses engulfed by microglia/macrophages. In agreement with the loss of inhibitory perisomatic synapses, we further found that Schaffer collateral feedforward inhibition but not excitation was impaired in CA2 pyramidal neurons and accompanied by a reduced spike output. Ultimately, we show that these electrophysiological changes were associated with an impaired encoding of social memories. Together, our findings identify CA2 as a critical circuit in demyelinated intrahippocampal lesions and memory dysfunctions in MS.

neuroscience↗

bioRxiv2019

Close-Range Interactions Favor Growth in Random-Paired Extracted Soil Bacteria

Species interactions at the cellular level are thought to govern the formation and functioning of microbial communities, but direct measurements of species interactions are difficult to perform between the hundreds of different species that constitute most microbial ecosystems. We developed a methodology to examine interactive growth of random cell pairs encapsulated inside 40-70 {micro}m diameter agarose beads. We focused on a sandy soil as a test microbial ecosystem. By using gentle washing procedures, we detached microbial cells from sand and encapsulated them either in the absence or presence of pure culture inoculants. We then tested whether inoculants had on average positive or negative effects on the growth of resident community members depending on the growth substrate. Surprisingly, all the tested inoculants (including Pseudomonas veronii 1YdBTEX2, Pseudomonas putida F1, Pseudomonas protegens CHA0 and Escherichia coli MG1655) stimulated the growth of 40-80 percent of sand-derived cells when grown pair-wise in close proximity (i.e., within the same bead). This was true essentially irrespective of the growth substrate. Beneficial inoculant-sand cell partnerships resulted in up to 100-fold increase in productivity of the sand cell partner and up to 100-fold decrease in that of the inoculant. However, the maximum productivity attained by inoculant-sand cell partners within beads did not surpass that of inoculants alone. Further surprisingly, random pairs of sand cells encapsulated within the same bead also benefited growth in comparison to individual sand cells in a mutualistic manner (i.e., productivity when grown together was greater than the sum of individual productivities), but less than productivities observed in partnerships with the tested inoculants. This suggests that partnerships between inoculants and sand cells are not so much characterized by competition for substrate as by carbon loss through metabolite provision of the inoculant to sand cells (competitive exploitation).

microbiology↗